The aims of this study were to reveal the magnitude of the differences in protein structures at a cellular level as well as protein utilization and availability among soybean meal (SBM), canola meal (CM), and rapeseed meal (RSM) as feedstocks in China. Experiments were designed to compare the three different types of feedstocks in terms of: 1) protein chemical profiles; 2) protein fractions partitioned according to Cornell Net Carbohydrate and Protein System; 3) protein molecular structures and protein second structures; 4) special protein compounds-amino acid (AA); 5) total digestible protein and energy values; 6) in situ rumen protein degradability and intestinal digestibility. The protein second structures were measured using FT/IR molecular spectroscopy technique. A summary chemical approach in NRC model was applied to analyze truly digestible protein. The results showed significant differences in both protein nutritional profiles and protein structure parameters in terms of α-helix, β-sheet spectral intensity and their ratio, and amide I, amide II spectral intensity and their ratio among SBM, CM and RSM. SBM had higher crude protein (CP) and AA content than CM and RSM. For dry matter (DM), SBM and CM had a higher DM content compared with RSM (P < 0.05), whereas no statistical significance was found between SBM and CM (P = 0.28). Effective degradability of CP and DM did not demonstrate significant differences among the three groups (P > 0.05). Intestinal digestibility of rumen undegradable protein measured by three-step in vitro method showed that there was significant difference (P = 0.05) among SBM, CM and RSM, which SBM was the highest and RSM was the lowest with CM in between. NRC modeling results showed that digestible CP content in SBM was significantly higher than that of CM and RSM (P < 0.05). This study suggested that SBM and CM contained similar protein value and availability for dairy cattle, while RSM had the lowest protein quality and utilization.